Hello Anh-Dao,
Thank you for searching the mailing list archives before asking your
question.
The genePredToPsl command needs a MySQL database to function:
usage:
genePredToPsl db file.gp fileOut.psl
Using your same filenames, this would be:
genePredToPsl -bedFormat db bedformatfile pslformatoutputfile
Where "db" is the database name, such as hg18. Many tools in the Genome
Browser source tree need access to a database. You could either set up
your own database and put the appropriate tables in it (in this case the
'chromInfo' table is needed), or you can use the public MySQL server:
http://genome.ucsc.edu/FAQ/FAQdownloads#download29
As described in the link above, you will need to put a file called
.hg.conf in your home directory that contains these lines:
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
I hope this answers your question. If you have further questions,
please feel free to email us again at [EMAIL PROTECTED]
--
Brooke Rhead
UCSC Genome Bioinformatics Group
Nguyen, Anh-Dao (NIH/NHGRI) [C] wrote:
> Hello,
>
> I would like to use the pslMap program.
> After reading the threads below, firstly, I need to convert my human's SNPs
> from BED format to PSL format using the genePredToPsl program
>
> http://www.soe.ucsc.edu/pipermail/genome/2006-May/010816.html
> http://www.soe.ucsc.edu/pipermail/genome/2007-November/015074.html
>
> genePredToPsl -bedFormat bedformatfile pslformatoutputfile
>
> e.g. bedformatfile has the following entries:
> chr6 32470491 32470780 BTNL2_NM_019602_exon_1 0 +
> chr6 32471793 32472141 BTNL2_NM_019602_exon_2 0 +
>
> I am not sure how to use the command line above correctly.
>
>
> Thanks for your help.
> Anh-Dao
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
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